Phyloinformatics Summer of Code 2011/Summaries

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Student software developers showcase their work

For the fifth summer in a row, NESCent offered a number of internships aimed at introducing students to open-source software development. This summer, eight interns from the 2011 Google Summer of Code™ program worked remotely on an evoinformatics project of their own choosing, each under the guidance of an experienced mentor. NESCent’s 2011 Summer of Code students included Jan Engelhardt, Alexandru Lucian Ginsca, Sarah Hird, Peter Hoffman, Daniel Packer, Andrei-Alin Popescu, Apurv Verma, and Laurel Yohe. Their projects ranged from manipulating next-generation sequencing data for population genetic analysis, to enabling a frequently-used alignment viewer to analyze non-coding RNAs, to generating human readable text that could be integrated into Encyclopedia of Life from ontologies containing phenotype data. As their profiles below demonstrate, the students put their summers to very good use!

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Student: Jan Engelhardt

Mentor(s): Jim Procter, Peter Troshin

Project: Extending Jalview’s support for handling RNA

Jalview is a frequently used alignment viewer. I implemented new features for the analysis of non-coding RNAs. The RNA structure viewer VARNA can now be used from within Jalview to analyze individual or consensus secondary structures. There is also a new structure consensus annotation row. I furthermore worked on fixing bugs in the existing code. __________________________

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Student: Kathryn Iverson (University of Michigan)

Mentor(s): David Kidd, Karen Cranston, Xianhua Liu, Bill Piel

Project: PhyloGeoRef - a library for implementing geophylogenies in KML and Google Earth

My Summer of Code project was to create a library in Java that generates geophylogenies in KML format, which can be displayed by Google Earth. A geophylogeny is a phylogenetic tree that shows a group of organisms' geographic and evolutionary distribution. The PhyloGeoRef library can take a phylogenetic tree and a list of coordinates and display it in 3D space with Google Earth.

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Student: Lauren Lui (UC Santa Cruz)

Mentor(s): Jim Procter, Albert Vilella

Project: Extending Jalview Capabilities to Support RNA Sequence Alignment Annotation and Secondary Structure Visualization

I added features to Jalview, a popular open-source platform-independent multiple sequence alignment editor and analysis platform, to aid annotation and visualization of RNA secondary structures. Jalview now has the ability to import existing RNA sequences and alignments from the RFAM database, support for RNA secondary structure visualization in alignments, and coloring schemes relevant to RNA alignments.

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Student: Anurag Priyam (Indian Institute of Technology Kharagpur)

Mentor(s): Rutger Vos, Jan Aerts

Project: Develop an API for NeXML I/O, and, RDF triples for BioRuby

BioRuby is an open-source code library for bioinformatics based on the Ruby programming language, RDF is a general-purpose standard for semantic annotation of data objects on the web, and NeXML is an XML-based, RDF-aware file format specifically for phylogenetic data. For my project, I added support for working with RDF and NeXML in BioRuby. I created an annotation module, built upon RDF, that provides methods to semantically annotate and query BioRuby objects, and a NeXML module that enables BioRuby users to work seamlessly with NeXML files. My code integrates into BioRuby's existing framework for manipulating phylogenetic and comparative data on molecules and morphology.

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Student: Conrad Stack (Pennsylvania State University)

Mentor(s): Brian O'Meara, Luke Harmon

Project: Ancestral State Reconstruction in R

RBrownie is a software package for the R Project for Statistical Computing. It is based on the Brownie core library, written in C++, for testing evolutionary hypotheses about the evolution of morphological and life history characters in the context of a phylogenetic tree. RBrownie merges this functionality with R's user-friendly coding environment. By adding new classes and a data processing function, my code extends R's capacity for comparative phylogenetic analyses.

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